PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size.

BMC Bioinformatics
Kristina Allen-BradyNicola J Camp

Abstract

We present a general approach to perform association analyses in pedigrees of arbitrary size and structure, which also allows for a mixture of pedigree members and independent individuals to be analyzed together, to test genetic markers and qualitative or quantitative traits. Our software, PedGenie, uses Monte Carlo significance testing to provide a valid test for related individuals that can be applied to any test statistic, including transmission disequilibrium statistics. Single locus at a time, composite genotype tests, and haplotype analyses may all be performed. We illustrate the validity and functionality of PedGenie using simulated and real data sets. For the real data set, we evaluated the role of two tagging-single nucleotide polymorphisms (tSNPs) in the DNA repair gene, NBS1, and their association with female breast cancer in 462 cases and 572 controls selected to be BRCA1/2 mutation negative from 139 high-risk Utah breast cancer families. The results from PedGenie were shown to be valid both for accurate p-value calculations and consideration of pedigree structure in the simulated data set. A nominally significant association with breast cancer was observed with the NBS1 tSNP rs709816 for carriage of the rare allele...Continue Reading

References

Jan 1, 1989·Genetic Epidemiology·J Ott
Jan 1, 1993·Statistical Methods in Medical Research·E Sobel, K Lange
Dec 10, 1997·Human Heredity·D Rabinowitz
Apr 16, 1998·American Journal of Human Genetics·R S Spielman, W J Ewens
Sep 16, 1998·Proceedings of the National Academy of Sciences of the United States of America·N E Morton, A Collins
Oct 30, 1998·American Journal of Human Genetics·S A MonksB S Weir
Jan 13, 2000·American Journal of Human Genetics·G R AbecasisW O Cookson
Mar 11, 2000·American Journal of Human Genetics·J S SinsheimerK Lange
May 29, 2000·American Journal of Human Genetics·E R MartinN L Kaplan
Jul 26, 2000·European Journal of Human Genetics : EJHG·G R AbecasisL R Cardon
Mar 20, 2001·American Journal of Human Genetics·E R MartinN L Kaplan
Apr 6, 2001·Journal of Medical Genetics·P MaraschioL Tiepolo
May 16, 2001·American Journal of Human Genetics·S L Slager, D J Schaid
Jan 17, 2002·Genetic Epidemiology·L AlmasyJ Blangero
Jan 25, 2002·Annals of Human Genetics·J C Whittaker, A P Morris
Feb 13, 2002·American Journal of Medical Genetics·Thomas G Schulze, Francis J McMahon
Feb 22, 2002·Theoretical Population Biology·D B Allison, M C Neale
May 25, 2002·Human Molecular Genetics·Bettina KuschelAlison Dunning
Oct 22, 2002·American Journal of Human Genetics·Daniel J SchaidStephen N Thibodeau
Jul 8, 2003·International Journal of Cancer. Journal International Du Cancer·Bohdan GórskiJan Lubiński
Feb 21, 2004·BMC Genetics·Michael D BadziochGail P Jarvik
Mar 31, 2004·Nature Genetics·Jonathan MarchiniPeter Donnelly
Jun 9, 2004·International Journal of Cancer. Journal International Du Cancer·Jan SteffenKarl Sperling
Jul 20, 2004·Chromosoma·Kenta IijimaHiroshi Tauchi
Aug 4, 2004·Journal of Bioinformatics and Computational Biology·Jing Li, Tao Jiang
Aug 7, 2004·Bioinformatics·J C BarrettM J Daly
Oct 16, 2004·European Journal of Human Genetics : EJHG·Ruzong FanJeeSun Jung
Dec 4, 2004·Genetic Epidemiology·Sharon R BrowningMichael J Wagner
Dec 21, 2004·Nature Genetics·Agnar HelgasonKári Stefánsson
Jun 28, 2005·Breast Cancer Research and Treatment·B GórskiJ Lubiński
Jul 26, 2005·Nature Genetics·Catarina D CampbellJoel N Hirschhorn
May 22, 2008·Genetics·Jonathan P BollbackRasmus Nielsen

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Citations

Oct 3, 2007·Osteoporosis International : a Journal Established As Result of Cooperation Between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA·T ForoudM J Econs
Nov 16, 2010·Bioinformatics·Ryan AboNicola J Camp
Mar 14, 2013·Journal of the National Cancer Institute·Dan ChenUlf Gyllensten
Jun 3, 2011·Journal of Medical Genetics·Wei-Yu LinAngela Cox
Mar 26, 2009·Cancer Research·Neil Duncan ShephardAngela Cox
Apr 2, 2009·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Nicola J CampLisa A Cannon-Albright
Jan 22, 2009·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Karen CurtinUNKNOWN Colorectal Cancer Study Group
May 9, 2009·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Mia M GaudetUNKNOWN Breast Cancer Association Consortium
Aug 20, 2009·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Karen CurtinUNKNOWN Colorectal Cancer Study Group
Nov 17, 2007·BMC Bioinformatics·Karen CurtinNicola J Camp
Mar 1, 2008·BMC Bioinformatics·Kristin K Nicodemus
May 10, 2008·BMC Proceedings·Karen CurtinNicola J Camp
Mar 1, 2012·BMC Proceedings·Kristina Allen-BradyLisa Cannon-Albright
Nov 23, 2011·Obstetrics and Gynecology·Kristina Allen-BradyPeggy A Norton
Jul 4, 2012·Journal of Cancer Research and Clinical Oncology·Nina ErčuljVita Dolžan
Dec 5, 2009·Gynecologic Oncology·Emma L IvanssonUlf B Gyllensten
Aug 11, 2007·International Journal of Cancer. Journal International Du Cancer·Emma L IvanssonUlf B Gyllensten
Jul 2, 2009·American Journal of Hematology·Paola SebastianiMartin H Steinberg
Nov 7, 2015·Statistical Applications in Genetics and Molecular Biology·Alexandre Bureau, Thierry Duchesne
Mar 10, 2011·International Journal of Cancer. Journal International Du Cancer·Felipe A CastroMichael Pawlita
Jul 9, 2013·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Liesel M FitzgeraldJanet L Stanford

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Methods Mentioned

BETA
genotyping

Software Mentioned

Java
QTDT
GeneCounter
GeneCountAllele
PedGenie
GENEHUNTER

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